In interviews, the women described being locked in houses by the dozen, at the beck and call of fighters who forced them to have sex, sometimes with the specific goal of impregnating them.

“They married me,” said Hamsatu, 25, a young woman in a black-and-purple head scarf, looking down at the ground. She said she was four months pregnant, that the father was a Boko Haram member and that she had been forced to have sex with other militants who took control of her town.

“They chose the ones they wanted to marry,” added Hamsatu, whose full name was not used to protect her identity. “If anybody shouts, they said they would shoot them.”

Boko Haram, a radical Islamist sect that has taken over large stretches of territory in the country’s northeast, has long targeted women, rounding them up as it captures towns and villages. Women and girls have been given to Boko Haram fighters for “marriage,” a euphemism for the sexual violence that occurs even when unions are cloaked in religion.

Now, dozens of newly freed women and girls, many of them pregnant and battered, are showing up at a sprawling camp for the displaced here outside the Borno State capital, Maiduguri, as Nigerian soldiers and other military forces try to push Boko Haram out of nearby territory it has occupied for much of the past year.

The full human toll of that occupation is only now emerging. More than 15,000 people have sought shelter at the camp, at an abandoned federal office-worker training center, most of them women, relief officials said. Over 200 have so far been found to be pregnant, but relief officials believe many more are bearing the unwanted children of Boko Haram militants.

“The sect leaders make a very conscious effort to impregnate the women,” said the Borno governor, Kashim Shettima. “Some of them, I was told, even pray before mating, offering supplications for God to make the products of what they are doing become children that will inherit their ideology.”

The militants have openly promised to treat women as chattel. After Boko Haram militants kidnapped nearly 300 schoolgirls from the village of Chibok last year, the group’s leader called them slaves and threatened to “sell them in the market.”

“We would marry them out at the age of 9,” the leader, Abubakar Shekau, said in a video message soon after the girls were abducted, prompting the global “Bring Back Our Girls” campaign. “We would marry them out at the age of 12.”

As the group has lost control of towns and thousands of people have fled in recent weeks, a grim picture of that treatment has emerged: hundreds of women and girls as young as 11 subjected to systematic, organized sexual violence.

Yahauwa, 30, used her green head scarf to wipe away tears as she clutched a plastic bag full of medicine. She had just tested positive for H.I.V.

“Is it from the people who forced me to have affairs with them?” she asked a relief worker, tears streaming down her face.

Later, she explained that she and many other women had been “locked in one big room.”

“When they came, they would select the one they wanted to sleep with,” she said. “They said, ‘If you do not marry us, we will slaughter you.’ ”

As the women spoke, two trucks crammed with more people arrived at the rudimentary camp guarded by watchful soldiers. Even the local news media is kept out.

Many of the residents of the camp spend the day outside in blazing 100-degree-plus heat here. They dare not return home.

Boko Haram is now on the retreat, but the countryside is not secure. People from several towns said the militants had not been defeated, as the Nigerian military maintains, but had simply fled as troops advanced with superior firepower.

Indeed, Maiduguri itself, a city of more than two million, came under attack again from Boko Haram last week. The militants tried to storm a military base and were pushed back only after hours of what residents said was heavy shooting by the military. On Saturday, a suicide bomber, a young girl, killed at least seven people in nearby Damaturu, and officials said the insurgents had recaptured the town of Marte.

The humiliation of what the refugees have been through led many of the women interviewed at the camp to deny being abused by the militants. But relief workers here said that when they arrived, many acknowledged that they had been raped.

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Fanna, a delicate 12-year-old who had arrived at the camp here three days before, crouched on the floor, clasping her knees, and insisted in her thin child’s voice that Boko Haram had not touched her. Relief officials said that in her camp entry interview, she, too, had said she was raped by the militants.

Now, many officials worry about the long-term health effects of the abuse. Yana, a young woman wearing sparkling golden bangles, said the fighters had “parked” her — a word many women have used to describe their imprisonment — with about 50 other women in a house in Bama, Borno State’s second city, with a population of several hundred thousand. Bama was occupied by Boko Haram last September.

Inside the house, “If they want to have an affair with a woman, they will just take her to a private place, so that the others won’t see,” said Yana in a singsong voice. She could not recall her age; a relief worker at the camp here said she had been raped so often by Boko Haram that she was “psychologically affected.”

Yana said the militants had forced her to have sex with them.

Her feet and stomach were swollen and the relief worker said she was probably pregnant, though her test results had not yet come back. Other workers here said many of the women had signs of physical and psychological trauma from being repeatedly raped.

Nigerian officials have reacted gingerly as the evidence of large-scale sexual violence by Boko Haram emerges.

The federal government appeared to have a scant presence at the camp here, despite the thousands of small children, around a third of them parentless, and near-daily deaths from illness or malnutrition. Flocks of little children roam the camp, unwatched. On a recent morning, two small boys were brought into the camp clinic with serious cuts and burns.

Unicef, a few other international agencies and the state government are providing some help, but relief officials said some of the women were too traumatized to leave their tents to seek help in the clinic.

Officials in the nation’s capital, Abuja, have said little. A new government, led by the former strongman Muhammadu Buhari, will be seated this month.

But officials and relief workers here in Borno State, where Boko Haram was born and remains strongest, said the organized nature of Boko Haram’s sexual violence appeared to point to a deliberate self-perpetuation plan.

“It’s like they wanted to have their own siblings to take over from them,” said Abba Mohammed Bashir Shuwa, a senior state official in Maiduguri.

A relief official at the camp who is working closely with the abused women echoed that thought. “We are going to have another set of Boko Haram,” said the official, Hadiza Waziri. “Most of these women now, they don’t want these pregnancies. You cannot love the child.”

The militants’ fixation with capturing, hoarding and “marrying” the women allowed some to witness central elements in their military strategy.

Meriam, 36, who had just arrived at the camp in Maiduguri from Gwoza, a Boko Haram headquarters town, spoke of being imprisoned with dozens of other women, including some who were being trained as suicide bombers.

Increasingly over the past year, the terrorists have used women and children to carry out suicide bombings against civilian targets like markets.

“The Boko Haram would recite the prayer for the dead,” Meriam said. “Then they would put on the hijab,” covering the suicide belt.

After they had prepared, “They said, ‘God will forgive us,’ ” she said. “Then, they would enter the vehicles, and they would send the women away.”

Meriam said she had seen a few of the Chibok village girls at the hospital in Gwoza, and said that the Boko Haram appeared to give them a special status.

Back at the Dalori camp, Hamsat, a 16-year-old high school student from Bama who was wearing a delicate pink head scarf, clasped her hands tightly and looked down. No, she said, Boko Haram had not touched her. Others, yes, in the group of over 200, but not her.

“They were having affairs with them,” she said. “Others were very stubborn. I used to pray.”

Relief officials said that when she arrived two weeks ago, Hamsat was among those who acknowledged having been raped.

A version of this article appears in print on May 19, 2015, on Page A1 of the New York edition with the headline: Former Captives in Nigeria Tell of Mass Rapes. Order Reprints|Today's Paper|Subscribe